Evolutionary origins of lymphocytes: ensembles of T cell and B cell transcriptional regulators in a cartilaginous fish

Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species

INTRODUCTION

Both innate and adaptive immune system undergo evolution from low to high vertebrates. Due to the limitation of conventional approaches in identifying broader spectrum of immune cells and molecules from various vertebrates, it remains unclear how immune molecules evolve among vertebrates.

OBJECTIVES

Here, we utilized carry out comparative transcriptome analysis in various immune cells across seven vertebrate species.

METHODS

Single-cell RNA sequencing (scRNA-seq).

RESULTS

We uncovered both conserved and species-specific profiling of gene expression in innate and adaptive immunity. Macrophages exhibited highly-diversified genes and developed sophisticated molecular signaling networks along with evolution, indicating effective and versatile functions in higher species. In contrast, B cells conservatively evolved with less differentially-expressed genes in analyzed species. Interestingly, T cells represented a dominant immune cell populations in all species and unique T cell populations were identified in zebrafish and pig. We also revealed compensatory TCR cascade components utilized by different species. Inter-species comparison of core gene programs demonstrated mouse species has the highest similarity in immune transcriptomes to human.

CONCLUSIONS

Therefore, our comparative study reveals gene transcription characteristics across multiple vertebrate species during the evolution of immune system, providing insights for species-specific immunity as well as the translation of animal studies to human physiology and disease.

Comparative study of cartilaginous fish divulges insights into the early evolution of primary, secondary and mucosal lymphoid tissue architecture

Cartilaginous fish are located at a pivotal point in phylogeny where the adaptive immune system begins to resemble that of other, more-derived jawed vertebrates, including mammals. For this reason, sharks and other cartilaginous fish are ideal models for studying the natural history of immunity. Insights from such studies may include distinguishing the (evolutionarily conserved) fundamental aspects of adaptive immunity from the (more recent) accessory. Some lymphoid tissues of sharks, including the thymus and spleen, resemble those of mammals in both appearance and function. The cartilaginous skeleton of sharks has no bone marrow, which is also absent in bony fish despite calcified bone, but cartilaginous fish have other Leydig's and epigonal organs that function to provide hematopoiesis analogous to mammalian bone marrow. Conserved across all vertebrate phylogeny in some form is gut-associated lymphoid tissues, or GALT, which is seen from agnathans to mammals. Though it takes many forms, from typhlosole in lamprey to Peyer's patches in mammals, the GALT serves as a site of antigen concentration and exposure to lymphocytes in the digestive tract. Though more complex lymphoid organs are not present in agnathans, they have several primitive tissues, such as the thymoid and supraneural body, that appear to serve their variable lymphocyte receptor-based adaptive immune system. There are several similarities between the adaptive immune structures in cartilaginous and bony fish, such as the thymus and spleen, but there are mechanisms employed in bony fish that in some instances bridge their adaptive immune systems to that of tetrapods. This review summarizes what we know of lymphoid tissues in cartilaginous fishes and uses these data to compare primary and secondary tissues in jawless, cartilaginous, and bony fishes to contextualize the early natural history of vertebrate mucosal immune tissues.

Should we Try to Alleviate Immunosenescence and Inflammaging - Why, How and to What Extent?

With advancing age, immune responses of human beings to external pathogens, i.e., bacteria, viruses, fungi and parasites, and to internal pathogens - malignant neoplasm cells - become less effective. Two major features in the process of aging of the human immune system are immunosenescence and inflammaging. The immune systems of our predecessors co-evolved with pathogens, which led to the occurrence of effective immunity. However, the otherwise beneficial activity may pose problems to the organism of the host and so it has builtin brakes (regulatory immune cells) and - with age - it undergoes adaptations and modifications, examples of which are the mentioned inflammaging and immunosenescence. Here we describe the mechanisms that first created our immune systems, then the consequences of their changes associated with aging, and the mechanisms of inflammaging and immunosenescence. Finally, we discuss to what extent both processes are detrimental and to what extent they might be beneficial and propose some therapeutic approaches for their wise control.

A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish

The immune system is composed of two subsystems-the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates-the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.

Evolutionary intraembryonic origin of vertebrate hematopoietic stem cells in the elasmobranch spleen

The electric ray (Torpedo marmorata Risso) provides an animal model for the detection of early intraembryonic hemopoietic stem cells (HSCs) in sea vertebrates. The spleen of this bone-marrowless vertebrate appears to be the major site of HSCs differentiation during development and in adulthood. Splenic development in this species was investigated and hemopoietic stem cells were detected in this organ by immunocytochemistry utilizing CD34 and CD38 antibodies. At stage I (2-cm-long embryos with external gills), the spleen contains only mesenchymal cells. At stage II (3-4 cm-long embryos with a discoidal shape and internal gills), an initial red pulp was observed in the spleen, without immunostained cells. At stage III (10-11- cm-long embryos), the spleen contained well-developed white pulp, red pulp and ellipsoids. Image analysis at stage III showed four cell populations, i.e. CD34+/CD38-, CD34+/CD38+, CD34- /CD38+, and CD34-/CD38- cells. The present findings, obtained from an elasmobranch, indicate that the CD34 and CD38 phenotypes are conserved through vertebrate evolution.

A role for the CXCR4-CXCL12 axis in the little skate, Leucoraja erinacea

The interaction between C-X-C chemokine receptor type 4 (CXCR4) and its cognate ligand C-X-C motif chemokine ligand 12 (CXCL12) plays a critical role in regulating hematopoietic stem cell activation and subsequent cellular mobilization. Extensive studies of these genes have been conducted in mammals, but much less is known about the expression and function of CXCR4 and CXCL12 in non-mammalian vertebrates. In the present study, we identify simultaneous expression of CXCR4 and CXCL12 orthologs in the epigonal organ (the primary hematopoietic tissue) of the little skate, Leucoraja erinacea. Genetic and phylogenetic analyses were functionally supported by significant mobilization of leukocytes following administration of Plerixafor, a CXCR4 antagonist and clinically important drug. Our results provide evidence that, as in humans, Plerixafor disrupts CXCR4/CXCL12 binding in the little skate, facilitating release of leukocytes into the bloodstream. Our study illustrates the value of the little skate as a model organism, particularly in studies of hematopoiesis and potentially for preclinical research on hematological and vascular disorders.

T Cell Receptor Activation of NF-κB in Effector T Cells: Visualizing Signaling Events Within and Beyond the Cytoplasmic Domain of the Immunological Synapse

The T cell receptor (TCR) to NF-κB signaling pathway plays a critical role in regulation of proliferation and effector T cell differentiation and function. In naïve T cells, data suggest that most or all key cytoplasmic NF-κB signaling occurs in a TCR-proximal manner at the immunological synapse (IS). However, the subcellular organization of cytoplasmic NF-κB-activating complexes in effector T cells is more complex, involving signaling molecules and regulatory mechanisms beyond those operative in naïve cells. Additionally, in effector T cells, much signaling occurs at cytoplasmic locations distant from the IS. Visualization of these cytoplasmic signaling complexes has provided key insights into the complex and dynamic regulation of NF-κB signal transduction in effector T cells. In this chapter, we provide in-depth protocols for activating and preparing effector T cells for fluorescence imaging, as well as a discussion of the effective application of distinct imaging methodologies, including confocal and super-resolution microscopy and imaging flow cytometry.

Putting J chain back on the map: how might its expression define plasma cell development?

Joining chain (J chain) is a small polypeptide that regulates multimerization of secretory IgM and IgA, the only two mammalian Igs capable of forming multimers. J chain also is required for poly-Ig receptor-mediated transport of these Ig classes across the mucosal epithelium. It is generally assumed that all plasma cells express J chain regardless of expressed isotype, despite the documented presence of J chain(-) plasma cells in mammals, specifically in all monomeric IgA-secreting cells and some IgG-secreting cells. Compared with most other immune molecules, J chain has not been studied extensively, in part because of technical limitations. Even the reported phenotype of the J chain-knockout mouse is often misunderstood or underappreciated. In this short review, we discuss J chain in light of the various proposed models of its expression and regulation, with an added focus on its evolutionary significance, as well as its expression in different B cell lineages/differentiation states.

SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods) and actinoptergii (ray-finned fish including teleosts) taxa, but limited for chondrichthyan fishes.  In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate.  SkateBase ( http://skatebase.org) serves as the skate genome project portal linking data, research tools, and teaching resources.

Origin and evolution of adaptive immunity

The evolutionary emergence of vertebrates was accompanied by major morphological and functional innovations, including the development of an adaptive immune system. Vertebrate adaptive immunity is based on the clonal expression of somatically diversifying antigen receptors on lymphocytes. This is a common feature of both the jawless and jawed vertebrates , although these two groups of extant vertebrates employ structurally different types of antigen receptors and principal mechanisms for their somatic diversification . These observations suggest that the common vertebrate ancestor must have already possessed a complex immune system, including B- and T-like lymphocyte lineages and primary lymphoid organs, such as the thymus, but possibly lacked the facilities for somatic diversification of antigen receptors. Interestingly, memory formation, previously considered to be a defining feature of adaptive immunity, also occurs in the context of innate immune responses and can even be observed in unicellular organisms, attesting to the convergent evolutionary history of distinct aspects of adaptive immunity.

B cell receptor accessory molecule CD79α: characterisation and expression analysis in a cartilaginous fish, the spiny dogfish (Squalus acanthias)

CD79α (also known as Igα) is a component of the B cell antigen receptor complex and plays an important role in B cell signalling. The CD79α protein is present on the surface of B cells throughout their life cycle, and is absent on all other healthy cells, making it a highly reliable marker for B cells in mammals. In this study the spiny dogfish (Squalus acanthias) CD79α (SaCD79α) is described and its expression studied under constitutive and stimulated conditions. The spiny dogfish CD79α cDNA contains an open reading frame of 618 bp, encoding a protein of 205 amino acids. Comparison of the SaCD79α gene with that of other species shows that the gross structure (number of exons, exon/intron boundaries, etc.) is highly conserved across phylogeny. Additionally, analysis of the 5' flanking region shows SaCD79α lacks a TATA box and possesses binding sites for multiple transcription factors implicated in its B cell-specific gene transcription in other species. Spiny dogfish CD79α is most highly expressed in immune tissues, such as spleen, epigonal and Leydig organ, and its transcript level significantly correlates with those of spiny dogfish immunoglobulin heavy chains. Additionally, CD79α transcription is up-regulated, to a small but significant degree, in peripheral blood cells following stimulation with pokeweed mitogen. These results strongly indicate that, as in mammals, spiny dogfish CD79α is expressed by shark B cells where it associates with surface-bound immunoglobulin to form a fully functional BCR, and thus may serve as a pan-B cell marker in future shark immunological studies.

Evolution of the immune system in the lower vertebrates

The evolutionary emergence of vertebrates was accompanied by the invention of adaptive immunity. This is characterized by extraordinarily diverse repertoires of somatically assembled antigen receptors and the facility of antigen-specific memory, leading to more rapid and efficient secondary immune responses. Adaptive immunity emerged twice during early vertebrate evolution, once in the lineage leading to jawless fishes (such as lamprey and hagfish) and, independently, in the lineage leading to jawed vertebrates (comprising the overwhelming majority of extant vertebrates, from cartilaginous fishes to mammals). Recent findings on the immune systems of jawless and jawed fishes (here referred to as lower vertebrates) impact on the identification of general principles governing the structure and function of adaptive immunity and its coevolution with innate defenses. The discovery of conserved features of adaptive immunity will guide attempts to generate synthetic immunological functionalities and thus provide new avenues for intervening with faulty immune functions in humans.

Characterisation and expression analysis of B-cell activating factor (BAFF) in spiny dogfish (Squalus acanthias): cartilaginous fish BAFF has a unique extra exon that may impact receptor binding

B-cell activating factor (BAFF), also known as tumour necrosis factor (TNF) ligand superfamily member 13B, is an important immune regulator with critical roles in B-cell survival, proliferation, differentiation and immunoglobulin secretion. A BAFF gene has been cloned from spiny dogfish (Squalus acanthias) and its expression studied. The dogfish BAFF encodes for an anchored type-II transmembrane protein of 288 aa with a putative furin protease cleavage site and TNF family signature as seen in BAFFs from other species. The identity of dogfish BAFF has also been confirmed by conserved cysteine residues, and phylogenetic tree analysis. The dogfish BAFF gene has an extra exon not seen in teleost fish, birds and mammals that encodes for 29 aa and may impact on receptor binding. The dogfish BAFF is highly expressed in immune tissues, such as spleen, and is up-regulated by PWM in peripheral blood leucocytes, suggesting a potentially important role in the immune system.

Dissecting teleost B cell differentiation using transcription factors

B cell developmental pathways in teleost fishes are poorly understood. In the absence of serological reagents, an alternative approach to dissecting teleost B cell development is to use transcription factors that are differentially expressed during B cell development. This review discusses the structure and function of six transcription factors that play essential roles during teleost B cell development: Ikaros, E2A, EBF, Pax5, Blimp1, and XbpI. Research on alternative splicing of both the Ikaros and Pax5 genes in rainbow trout is presented, including their functional significance. An application is discussed that should aid in elucidating teleost B cell development and activation, by using transcription factors as developmental markers in flow cytometric analysis. Possible future studies in teleost B cell development are suggested in the context of gene regulation. Lastly, broader impacts and practical applications are discussed.

E proteins and the regulation of early lymphocyte development

Lymphopoiesis generates mature B, T, and NK lymphocytes from hematopoietic stem cells via a series of increasingly restricted developmental intermediates. The transcriptional networks that regulate these fate choices are composed of both common and lineage-specific components, which combine to create a cellular context that informs the developmental response to external signals. E proteins are an important factor during lymphopoiesis, and E2A in particular is required for normal T- and B-cell development. Although the other E proteins, HEB and E2-2, are expressed during lymphopoiesis and can compensate for some of E2A's activity, E2A proteins have non-redundant functions during early T-cell development and at multiple checkpoints throughout B lymphopoiesis. More recently, a role for E2A has been demonstrated in the generation of lymphoid-primed multipotent progenitors and shown to favor their specification toward lymphoid over myeloid lineages. This review summarizes both our current understanding of the wide-ranging functions of E proteins during the development of adaptive lymphocytes and the novel functions of E2A in orchestrating a lymphoid-biased cellular context in early multipotent progenitors.

Description of an elasmobranch TCR coreceptor: CD8α from Rhinobatos productus

Cell-mediated immunity plays an essential role for the control and eradication of intracellular pathogens. To learn more about the evolutionary origins of the first signal (Signal 1) for T-cell activation, we cloned CD8α from an elasmobranch, Rhinobatos productus. Similar to full-length CD8α cDNAs from other vertebrates, Rhpr-CD8α (1800bp) encodes a 219 amino acid open reading frame composed of a signal peptide, an extracellular IgSF V domain and a stalk/hinge region followed by a well-conserved transmembrane domain and cytoplasmic tail. Overall, the mature Rhpr-CD8α protein (201 aa) displays ∼ 30% amino acid identity with mammalian CD8α including absolute conservation of cysteine residues involved in the IgSf V domain fold and dimerization of CD8αα and CD8αβ. One prominent feature is the absence of the LCK association motif (CXC) that is needed for achieving signal 1 in tetrapods. Both elasmobranch and teleost CD8α protein sequences possess a similar but distinctly different motif (CXH) in the cytoplasmic tail. The overall genomic structure of CD8α has been conserved during the course of vertebrate evolution both for the number of exons and phase of splicing. Finally, quantitative RTPCR demonstrated that elasmobranch CD8α is expressed in lymphoid-rich tissues similar to CD8 in other vertebrates. The results from this study indicate the existence of CD8 prior to the emergence of the gnathostomes (>450 MYA) while providing evidence that the canonical LCK association motif in mammals is likely a derived characteristic of tetrapod CD8α, suggesting potential differences for T-cell education and activation in the various gnathostomes.

Lesions associated with plerocerci (Platyhelminthes: Cestoda: Trypanorhyncha) in the gastric wall of a cownose ray, Rhinoptera bonasus (Mitchill), (Myliobatiformes: Rhinopteridae) from the northern Gulf of Mexico

We describe lesions associated with a seemingly intense infection of trypanorhynch plerocerci (Platyhelminthes: Cestoda: Trypanorhyncha) in the gastric wall of a female cownose ray, Rhinoptera bonasus (Myliobatiformes: Rhinopteridae) captured in the northern Gulf of Mexico. Grossly, the multitude of encapsulated, encysted plerocerci imparted a bumpy and cobbled appearance to the serosa of the stomach, and none was observed in any other tissue during routine parasitological necropsy. Histologically, the plerocerci were associated with severe intramural granulomatous gastritis, vascular ectasia and mesothelial polyposis with the exclusion of the mucosa. To our knowledge, this is the first published case study documenting platyhelminth-associated histopathological changes in the gastrointestinal tract of R. bonasus as well as that of the efficacy of immunocytochemical markers for smooth muscle actin, Factor VIII, S-100, and proliferating cell nuclear antigen in Myliobatiformes. It also may serve as a potential primer for much needed ecological investigations regarding the potential role of elasmobranchs as intermediate or 'paratenic' hosts in the life cycles of trypanorhynch cestodes.

Functional analysis of fish BCL-6 and Blimp-1 in vitro: transcriptional repressors for B-cell terminal differentiation in fugu (Takifugu rubripes)

The transcriptional repressors BCL-6 and Blimp-1 are key regulators of B-cell terminal differentiation in mammals. We have previously identified the BCL-6 gene and Blimp-1 gene in fugu (Takifugu rubripes). In the present report, we conducted a functional analysis of fugu BCL-6 and Blimp-1 by using a one-hybrid reporter assay with Gal4 fusion proteins and Gal4DBD luciferase reporter gene. Results from the reporter assays in mammalian cell lines (HeLa, HEK-293, CV-1 and NIH3T3) and the fish cell line EPC show that Gal4-BCL6 and Gal4-Blimp1 strongly repress the transcription of the luciferase gene in all cell lines. Furthermore, deletion analyses show that the N-terminal region of BCL-6 has transcriptional repression activity; the BTB/POZ domain is an especially potent repression domain. In contrast to BCL-6, although the N-acidic domain and PR domain are insufficient for repression, most functional motifs of Blimp-1 are associated with transcriptional repression. These results suggest that BCL-6 and Blimp-1 are functional transcriptional repressors in fugu and that they regulate B-cell terminal differentiation in fugu.

Comparative analyses of B cell populations in trout kidney and mouse bone marrow: establishing "B cell signatures"

This study aimed to identify the frequency and distribution of developing B cell populations in the kidney of the rainbow trout, using four molecular B cell markers that are highly conserved between species, including two transcription factors, Pax5 and EBF1, recombination-activating gene RAG1, and the immunoglobulin heavy chain mu. Three distinct B cell stages were defined: early developing B cells (CLP, pro-B, and early pre-B cells), late developing B cell (late pre-B, immature B, and mature B cells), and IgM-secreting cells. Developmental stage-specific, combinatorial expression of Pax5, EBF1, RAG1 and immunoglobulin mu was determined in trout anterior kidney cells by flow cytometry. Trout staining patterns were compared to a well-defined primary immune tissue, mouse bone marrow, and using mouse surface markers B220 and CD43. A remarkable level of similarity was uncovered between the primary immune tissues of both species. Subsequent analysis of the entire trout kidney, divided into five contiguous segments K1-K5, revealed a complex pattern of early developing, late developing, and IgM-secreting B cells. Patterns in anterior kidney segment K1 were most similar to those of mouse bone marrow, while the most posterior part of the kidney, K5, had many IgM-secreting cells, but lacked early developing B cells. A potential second B lymphopoiesis site was uncovered in segment K4 of the kidney. The B cell patterns, or "B cell signatures" described here provide information on the relative abundance of distinct developing B cell populations in the trout kidney, and can be used in future studies on B cell development in other vertebrate species.

Early B-cell factor regulates the expression of Hemokinin-1 in the olfactory epithelium and differentiating B lymphocytes

Hemokinin-1, encoded by the TAC4 gene, is a tachykinin most closely related to substance P. Previous studies have shown that TAC4 distinguishes itself from other tachykinins by its predominantly non-neuronal expression profile, particularly in cells of the immune system. Here we report for the first time that the highest levels of TAC4 expression are found in the olfactory epithelium. Furthermore, we identify olfactory neuron-specific transcription factor (Olf-1), also known as early B-cell factor (EBF), as a novel regulator of TAC4 expression. EBF present in the olfactory epithelium and in B cells binds to two sites in the TAC4 promoter and modulates expression in developing B cells. Our findings suggest a role for TAC4 in cell differentiation, and represent a regulatory bridge between the nervous system and the immune system.

Expression pattern of GATA-3 in embryonic and fetal human skin suggests a role in epidermal and follicular morphogenesis

BACKGROUND

The transcription factor GATA-3 was recently identified as a master regulator in the specification of the inner root sheath. Additionally, it seems to play a role in skin barrier physiology. p63 binds and transactivates the GATA-3 promoter. While the expression profile of GATA-3 is delineated for the mouse, little is known about its expression in the adult human hair follicle and no studies are published about its distribution during human cutaneous embryogenesis.

METHODS

We examined samples from embryonic, fetal and adult human skin for the expression of GATA-3 using immunohistochemistry.

RESULTS

GATA-3 is expressed late during human skin development. Its expression pattern is comparable to the mouse and confined to the Huxley layer and inner root sheath cuticle but sparing the Henle layer. In addition, GATA-3 localizes to the spinous cell layer of the interfollicular epidermis.

CONCLUSIONS

From the described expression pattern, it is highly probable that GATA-3 plays a role in follicular and epidermal morphogenesis. What the anatomically confined expression of GATA-3 to the spinous layer means biologically for the physiology of the skin is still unclear. Likewise, it still needs to be shown if GATA-3 could be exploited in the diagnosis of adnexal neoplasms.

Transcription factor expression dynamics of early T-lymphocyte specification and commitment

Mammalian T lymphocytes are a prototype for development from adult pluripotent stem cells. While T-cell specification is driven by Notch signaling, T-lineage commitment is only finalized after prolonged Notch activation. However, no T-lineage specific regulatory factor has been reported that mediates commitment. We used a gene-discovery approach to identify additional candidate T-lineage transcription factors and characterized expression of >100 regulatory genes in early T-cell precursors using realtime RT-PCR. These regulatory genes were also monitored in multilineage precursors as they entered T-cell or non-T-cell pathways in vitro; in non-T cells ex vivo; and in later T-cell developmental stages after lineage commitment. At least three major expression patterns were observed. Transcription factors in the largest group are expressed at relatively stable levels throughout T-lineage specification as a legacy from prethymic precursors, with some continuing while others are downregulated after commitment. Another group is highly expressed in the earliest stages only, and is downregulated before or during commitment. Genes in a third group undergo upregulation at one of three distinct transitions, suggesting a positive regulatory cascade. However, the transcription factors induced during commitment are not T-lineage specific. Different members of the same transcription factor family can follow opposite trajectories during specification and commitment, while factors co-expressed early can be expressed in divergent patterns in later T-cell development. Some factors reveal new regulatory distinctions between alphabeta and gammadelta T-lineage differentiation. These results show that T-cell identity has an essentially complex regulatory basis and provide a detailed framework for regulatory network modeling of T-cell specification.

Molecular mechanisms that control mouse and human TCR-alphabeta and TCR-gammadelta T cell development

Following specification of hematopoietic precursor cells into the T cell lineage, several developmental options remain available to the immature thymocytes. The paradigm is that the outcome of the T cell receptor rearrangements and the corresponding T cell receptor signaling events will be predominant to determine the first of these choices: the alphabeta versus gammadelta T cell pathways. Here, we review the thymus-derived environmental signals, the transcriptional mediators, and other molecular mechanisms that are also involved in this decision in both the mouse and human. We discuss the differences in cellular events between the alphabeta and gammadelta developmental pathways and try to correlate these with a corresponding complexity of the molecular mechanisms that support them.

Evolution of a core gene network for skeletogenesis in chordates

The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin. In mammals the Runt genes are central regulators of skeletogenesis. Runx2 was shown to be essential for osteoblast differentiation, tooth development, and bone formation. Both Runx2 and Runx3 are essential for chondrocyte maturation. Furthermore, Runx2 directly regulates Indian hedgehog expression, a master coordinator of skeletal development. To clarify the correlation of Runt gene evolution and the emergence of cartilage and bone in vertebrates, we cloned the Runt genes from hagfish as representative of jawless fish (MgRunxA, MgRunxB) and from dogfish as representative of jawed cartilaginous fish (ScRunx1-3). According to our phylogenetic reconstruction the stem species of chordates harboured a single Runt gene and thereafter Runt locus duplications occurred during early vertebrate evolution. All newly isolated Runt genes were expressed in cartilage according to quantitative PCR. In situ hybridisation confirmed high MgRunxA expression in hard cartilage of hagfish. In dogfish ScRunx2 and ScRunx3 were expressed in embryonal cartilage whereas all three Runt genes were detected in teeth and placoid scales. In cephalochordates (lancelets) Runt, Hedgehog and SoxE were strongly expressed in the gill bars and expression of Runt and Hedgehog was found in endo- as well as ectodermal cells. Furthermore we demonstrate that the lancelet Runt protein binds to Runt binding sites in the lancelet Hedgehog promoter and regulates its activity. Together, these results suggest that Runt and Hedgehog were part of a core gene network for cartilage formation, which was already active in the gill bars of the common ancestor of cephalochordates and vertebrates and diversified after Runt duplications had occurred during vertebrate evolution. The similarities in expression patterns of Runt genes support the view that teeth and placoid scales evolved from a homologous developmental module.

GATA3 mRNA in ginbuna crucian carp (Carassius auratus langsdorfii): cDNA cloning, splice variants and expression analysis

GATA3, a transcriptional activator, plays a critical role in the development of T-cells and differentiation to T helper type 2 cells. To date, no information is available on the role of GATA3 in the teleost immune system. We identified full-length cDNA and alternatively spliced variants of ginbuna crucian carp GATA3 (gbGATA3). The gbGATA3 gene is transcribed into multiple splice variants lacking either one or both zinc finger domains, although the sequences of both domains are fully conserved between ginbuna and other vertebrates. We found that alternative splice site and stop codon in gbGATA3 intron 3, located between exons that separately encode the two zinc finger domains, are conserved among teleosts, suggesting that teleost GATA3 gene can be translated into multiple isoforms. RT-PCR analysis revealed that the gbGATA3 is strongly expressed in the brain, thymus and gill of unstimulated fish. Moreover, gbGATA3 expression was detected in surface-IgM-negative lymphocytes among kidney cells sorted by FACS. Real-time PCR demonstrated that expression levels of full-length gbGATA3 and the splice variants differed with tissue type, but full length was always the predominantly expressed form. These results suggest that gbGATA3, including its splice variants, is involved in teleost T-cell function.

Characterization and expression of the transcription factor PU.1 during LPS-induced inflammation in the rainbow trout (Oncorhynchus mykiss)

The transcription factor PU.1 plays a key role in hematopoietic lineage development and therefore in determining immune cell fate. A full length cDNA transcript of 1237 nucleotides encoding a highly conserved putative protein of 293 amino acids was identified by EST analysis in lipopolysaccharide (LPS) activated trout macrophages. Phylogenetic analyses highlight the significant level of structural conservation of the PU.1 transcription factor reinforcing the importance of this molecule in animal immunity. In trout, the PU.1 mRNA shows a tissue-specific expression pattern and is induced in vivo by LPS in muscle, liver, intestine and brain. Furthermore PU.1 is highly expressed in trout macrophages in primary culture. In situ expression analysis in the head kidney describes a large number of PU.1+ve cells distributed through the tissue in both LPS-treated and control animals. Cellular proliferation examined by BrdU immunohistochemistry (IHC) shows that LPS regulates hematopoietic processes in adult fish by stimulating cellular proliferation 3 days after treatment. These studies provide initial insights into hematopoietic/cellular processes in the head kidney of rainbow trout after in vivo LPS challenge.

Determinants of lymphoid-myeloid lineage diversification

In recent years, investigators have made great progress in delineating developmental pathways of several lymphoid and myeloid lineages and in identifying transcription factors that establish and maintain their fate. However, the developmental branching points between these two large cell compartments are still controversial, and little is known about how their diversification is induced. Here, we give an overview of determinants that play a role at lymphoid-myeloid junctures, in particular transcription factors and cytokine receptors. Experiments showing that myeloid lineages can be reversibly reprogrammed into one another by transcription factor network perturbations are used to highlight key principles of lineage commitment. We also discuss experiments showing that lymphoid-to-myeloid but not myeloid-to-lymphoid conversions can be induced by the enforced expression of a single transcription factor. We close by proposing that this asymmetry is related to a higher complexity of transcription factor networks in lymphoid cells compared with myeloid cells, and we suggest that this feature must be considered when searching for mechanisms by which hematopoietic stem cells become committed to lymphoid lineages.

B cell heterogeneity in the teleost kidney: evidence for a maturation gradient from anterior to posterior kidney

The fish immune system is quite different from the mammalian system because the anterior kidney forms the main site for hematopoiesis in this species. Using transcription factor-specific Abs derived from the murine system, together with anti-trout Ig Abs and Percoll gradient separation, we analyzed B cells from trout kidney sections and compared them to those from spleen and blood. For this study, immune cells were separated by Percoll gradients, and the resulting subpopulations were defined based on expression of B cell-specific transcription factors Pax-5 and B lymphocyte-induced maturation protein-1, as well as proliferative and Ig-secreting properties. Comparison of kidney, blood, and spleen B cell subsets suggest that 1) the anterior kidney contains mostly proliferating B cell precursors and plasma cells; 2) posterior kidney houses significant populations of (partially) activated B cells and plasmablasts; and 3) trout blood contains resting, non-Ig-secreting cells and lacks plasma cells. After LPS induction of resting B cells in vitro, the kidney and spleen have a high capacity for the generation of plasma cells, whereas the blood has virtually none. Our results indicate that trout B cell subsets are profoundly different among blood, anterior kidney, posterior kidney, and spleen. We hypothesize that developing B cells mature in the anterior side of the kidney and then migrate to sites of activation, either the spleen or the posterior kidney. Lastly, our data support the notion that the trout kidney is a complex, multifunctional immune organ with the potential to support both hemopoiesis as well as humoral immune activation.

Delayed, asynchronous, and reversible T-lineage specification induced by Notch/Delta signaling

Using the OP9-DL1 system to deliver temporally controlled Notch/Delta signaling, we show that pluripotent hematolymphoid progenitors undergo T-lineage specification and B-lineage inhibition in response to Notch signaling in a delayed and asynchronous way. Highly enriched progenitors from fetal liver require > or =3 d to begin B- or T-lineage differentiation. Clonal switch-culture analysis shows that progeny of some single cells can still generate both B- and T-lineage cells, after 1 wk of continuous delivery or deprivation of Notch/Delta signaling. Notch signaling induces T-cell genes and represses B-cell genes, but kinetics of activation of lineage-specific transcription factors are significantly delayed after induction of Notch target genes and can be temporally uncoupled from the Notch response. In the cells that initiate T-cell differentiation and gene expression most slowly in response to Notch/Delta signaling, Notch target genes are induced to the same level as in the cells that respond most rapidly. Early lineage-specific gene expression is also rapidly reversible in switch cultures. Thus, while necessary to induce and sustain T-cell development, Notch/Delta signaling is not sufficient for T-lineage specification and commitment, but instead can be permissive for the maintenance and proliferation of uncommitted progenitors that are omitted in binary-choice models.

Genes "waiting" for recruitment by the adaptive immune system: the insights from amphioxus

In seeking evidence of the existence of adaptive immune system (AIS) in ancient chordate, cDNA clones of six libraries from a protochordate, the Chinese amphioxus, were sequenced. Although the key molecules such as TCR, MHC, Ig, and RAG in AIS have not been identified from our database, we demonstrated in this study the extensive molecular evidence for the presence of genes homologous to many genes that are involved in AIS directly or indirectly, including some of which may represent the putative precursors of vertebrate AIS-related genes. The comparative analyses of these genes in different model organisms revealed the different fates of these genes during evolution. Their gene expression pattern suggested that the primitive digestive system is the pivotal place of the origin and evolution of the AIS. Our studies support the general statement that AIS appears after the jawless/jawed vertebrate split. However our study further reveals the fact that AIS is in its twilight in amphioxus and the evolution of the molecules in amphioxus are waiting for recruitment by the emergence of AIS.

Molecular genetics of T cell development

T cell development is guided by a complex set of transcription factors that act recursively, in different combinations, at each of the developmental choice points from T-lineage specification to peripheral T cell specialization. This review describes the modes of action of the major T-lineage-defining transcription factors and the signal pathways that activate them during intrathymic differentiation from pluripotent precursors. Roles of Notch and its effector RBPSuh (CSL), GATA-3, E2A/HEB and Id proteins, c-Myb, TCF-1, and members of the Runx, Ets, and Ikaros families are critical. Less known transcription factors that are newly recognized as being required for T cell development at particular checkpoints are also described. The transcriptional regulation of T cell development is contrasted with that of B cell development, in terms of their different degrees of overlap with the stem-cell program and the different roles of key transcription factors in gene regulatory networks leading to lineage commitment.

Origins of lymphocyte developmental programs: transcription factor evidence

This review explores the evolutionary origins of lymphocyte development by focusing on the transcription factors that direct mammalian lymphocyte development today. Gene expression data suggest that the programs to make lymphocytes involve the same transcription factor ensembles in all animals with lymphocytes. Most of these factors, GATA, Runx, PU.1/Spi, EBF/Olf, Ikaros, and Pax-2/5/8 family members, are also encoded in the genomes of animals without lymphocytes. We consider the functions of these factors in animals without lymphocytes in terms of discrete program components, which could have been assembled in a new way to create the lymphocyte developmental program approximately 500 My ago.